I don't have answer for your questions, but just FYI: AmberTools16 is free
with very simple download process
and you can perform simulation with sander
http://ambermd.org/AmberTools16-get.html
There is also corresponding manual here:
http://ambermd.org/doc12/Amber16.pdf
You can read it while waiting for feedback from others.
cheers
Hai
On Tue, Jul 12, 2016 at 11:36 AM, Vivien Ramothe <ramothe.vivien.gmail.com>
wrote:
> Hi,
> I'm a PHD student since a couple of month, and i have some troubles using
> CP2K,
> since it doesn't work for performing NVT simulation on molecules that have
> a virtual site.
> I'd like to perform molecular dynamics with AMBER i don't have the license
> yet.
> In order to know if it will be useful form me to take a license i need to
> know if
> there is a way to use the parameters i have for the atoms i use.
> The parameters that have been calculated for dispersion potential are made
> to be
> used with the Born Mayer potential: V(r)=f6*(C6/r6)+f8/(C8/r8),
> the f6 and f8 function are Tang Toennis damping functions.
> I'm reading the user manual since quite a few days now,
> even if if didn't see anything about this kind of potential in it.
> It seems i found a way to implement it myself by using the minimize option,
> of parmed command. but i'm not sure about it since i never used it one my
> own.
> Could you tell me please if it is possible to implement my own kind of
> potential?
> Does the parmed command work on every steps on the trajectory?
> How are the long range correction calculated on a potential that AMBER
> doesn't konw?
> And if Amber encountered the same kind of problems than CP2K with virtual
> site?
> Thank you
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> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
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Received on Tue Jul 12 2016 - 10:00:02 PDT
